Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis

Abstract

The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

Fig 1. Gene map and organization of the complete mitochondrial genome of C. globiceps.

Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content.

Fig 2. Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.

Fig 3. Evolutionary rates of C. globiceps mitogenome.

The rate of non-synonymous substitutions (Ka), the rate of synonymous substitutions (Ks) and the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions (Ka/Ks) for each protein-coding gene.

Fig 4. Overall mean p-genetic distance of six Macrouridae species for each of 13 protein genes.

They were calculated based on the first and second nucleotide positions and on the third nucleotide position of amino acid codons, and on the full sequence among six Macrouridae species, respectively.

Fig 5. Intergenic T-P spacer sequence of five Gadiform species.

Gm: Gadus morhua, Tc: Theragra chalcogramma, Bs: Boreogadus saida, Cg: Cetonurus globiceps, Vg: Ventrifossa garmani. Dots indicate identical positions and dashes indicate deletions. Conserved regions and tRNAs are marked by boxes.

Fig 6. Secondary structure prediction for the T-P spacer DNA sequence of C. globiceps.

Fig 7. Features present in the putative control region of C. globiceps mitogenome.

The conserved motifs ATGTA and its complement TACAT which may form thermostable hairpin structure are shaded. The conserved sequence blocks containing CSB-F, CSB-D, CSB-1,CSB-2 and CSB-3 are underlined and labeled by name. The arrows above the nucleotides indicate the tandem repeats.

Fig 8. Phylogenetic tree of Gadiform species reconstructed from concatenated DNA sequences of mitochondrial protein-coding genes.

Twelve mitochondrial protein-coding genes (with the exception of ND6) were used for the phylogenetic tree, which was produced by Bayesian inferences (BI). Sardinops melanostictus was used as the outgroup. Bayesian posterior probability are shown orderly on the nodes. The asterisk indicates the sequence generated in this study.